Although the apps, popular among the country's elite, were still working on private telecom operators on Friday, customers of Salaam Telecom, a government-owned service provider, reported that both apps had stopped working for them, The New York Times reported late Friday.
"It is wrong and illegal," Abdul Mujeeb Khalvatgar, executive director of Nai, a group that campaigns for free speech, was quoted as saying.
According to the Constitution, freedom of expression is inviolable in Afghanistan.
"WhatsApp and Telegram are tools of free speech -- if the government bans them, it means that tomorrow they could stand against media in Afghanistan too," he added.
The clarity on the reason for the temprory ban was not obtained but on Thursday, the deputy director of the telecoms regulatory authority told the BBC that the ban was due to "security concerns".
WhatsApp and Telegram are often used by the Taliban and other militant groups to evade government surveillance, the report said.
An official from the Ministry of Communications and Information Technology said that the request on the 20-day ban had come from the National Directorate of Security, the country's intelligence agency.
The ministry said that the apps were being temporarily banned "to introduce a new kind of technology", because users had complained about the quality of WhatsApp's service.
It also denied that the ban constituted a threat to freedom of expression.
"WhatsApp and Telegram are just applications for contact and the sending of audio messages, and this does not affect freedom of speech," the ministry added.